Few days ago Nitrado updated their servers to jk2mv 1.1
Now I have the problem that both servers are only visible in the serverlist when I use JK2MV clientside.
If I use basejk2, I'm unable to see them.

I think the ravensoft master was unreachable for me sometime in the last 24 hours. After issues with the raven masterserver some servers tend to not appear until they were completly restarted once (not just a mapchange, but really quit). Maybe you should try that. If that doesn't help check if your server shows up as protocol 0 (zero): Protocol Zero list [masterjk2.ravensoft.com]
The raven master sometimes sorts servers as protocol zero. If it does it usually helps to keep the server offline for 15 - 30 minutes.